From 5d0a91cc4fe4fd1ed74fd128ff6d2aee090599b6 Mon Sep 17 00:00:00 2001 From: Geert van Geest Date: Mon, 28 Mar 2022 09:18:19 +0200 Subject: [PATCH] closes #4 --- docs/day2/filtering_evaluation.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/day2/filtering_evaluation.md b/docs/day2/filtering_evaluation.md index bfb053e..15bf632 100644 --- a/docs/day2/filtering_evaluation.md +++ b/docs/day2/filtering_evaluation.md @@ -28,24 +28,24 @@ cd ~/workdir gatk SelectVariants \ --variant variants/trio.vcf \ ---select-type SNP \ +--select-type-to-include SNP \ --output variants/trio.SNP.vcf ``` **Exercise:** Check out the [documentation of `gatk SelectVariants`](https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants), and: -* Figure out what you'll need to fill in at `--select-type` if you want to select only INDELS. +* Figure out what you'll need to fill in at `--select-type-to-include` if you want to select only INDELS. * Generate a vcf with only the SNPs and a second vcf with only the INDELs from `trio.vcf`. ??? done "Answer" - You will need to fill in `INDEL` at `--select-type` to filter for INDELs. + You will need to fill in `INDEL` at `--select-type-to-include` to filter for INDELs. - To get the SNPs you can run the command above. To get the INDELs you'll need to change `--select-type` to `INDEL`: + To get the SNPs you can run the command above. To get the INDELs you'll need to change `--select-type-to-include` to `INDEL`: ```sh gatk SelectVariants \ --variant variants/trio.vcf \ - --select-type INDEL \ + --select-type-to-include INDEL \ --output variants/trio.INDEL.vcf ``` @@ -234,7 +234,7 @@ gatk Concordance \ !!! note We did the filtering on `trio.vcf`, therefore, you first have to extract the records that only apply to the mother by using `gatk SelectVariants`. - Also note that `trio.vcf` contains records other than SNPs and INDELs. Use `--select-type` to select only SNPs and INDELs. + Also note that `trio.vcf` contains records other than SNPs and INDELs. Use `--select-type-to-include` to select only SNPs and INDELs. ??? done "Answer" @@ -246,8 +246,8 @@ gatk Concordance \ --sample-name mother \ --exclude-non-variants \ --remove-unused-alternates \ - --select-type INDEL \ - --select-type SNP \ + --select-type-to-include INDEL \ + --select-type-to-include SNP \ --output variants/mother.trio.vcf ```